Type 1A diabetes is a complex genetic disease with a growing incidence. Improved prediction of type 1 diabetes will allow better prevention of severe symptoms at disease-onset and would facilitate clinical prevention trials. Type 1 diabetes is strongly associated with the major histocompatibility complex (MHC) on chromosome 6, but linkage disequilibrium in this genetic region complicates efforts to localize disease-associated genes. This book explores the strong genetic association between type 1 diabetes and the MHC and illustrates the importance of taking the extended linkage disequilibrium of conserved haplotypes into account with genetic analyses of the MHC. This book also demonstrates evidence for a genetic association between type 1 diabetes and a region telomeric of the traditional MHC. The MHC region is associated with many autoimmune diseases and this book, although focused on type 1 diabetes, may be of interest to anyone who wants to learn more about the genetics of the MHC and autoimmune diseases. This book should also be informational to those with an interest in molecular evolution.